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The SATA drives will always be master since they are on their own channels.
The IDE drive is also fine as master, or slave. It doesn't really matter...
As far as the OS is concerned, as long as you have the correct drive selected as your boot drive in the BIOS you'll be fine.
I've got three hard drives in my system, when I'm reformatting or installing windows I'll usually unplug the extra drives just to make sure I'm not screwing around with the wrong one.
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